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				<li  class="selection_button"><a href="#results" title="Input Data">Results</a></li>
					<li class="selection_button_span"><a>Selection</a></li>

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			<ul>
				<#if isAIC == 1>
					<li  class="selection_button">
				<#else>
					<li  class="selection_button_na">
				</#if>
					<a href="#aic" title="AIC">AIC</a></li>
				<#if isAICc == 1>
					<li  class="selection_button">
				<#else>
					<li  class="selection_button_na">
				</#if>
					<a href="#aicc" title="AICc">AICc</a></li>
				<#if isBIC == 1>
					<li  class="selection_button">
				<#else>
					<li  class="selection_button_na">
				</#if>
					<a href="#bic" title="BIC">BIC</a></li>
				<#if isDT == 1>
					<li  class="selection_button">
				<#else>
					<li  class="selection_button_na">
				</#if>
					<a href="#dt" title="DT">DT</a></li>
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<div id="program-meta">
	<h1><a name="program-meta"></a>Application Meta</h1>
	<h3>jModeltest 2.1</h3>
	(c) 2011-onwards D. Darriba, G.L. Taboada, R. Doallo and D. Posada,<br/>
    (1) Department of Biochemistry, Genetics and Immunology<br/>
        University of Vigo, 36310 Vigo, Spain.<br/>
    (2) Department of Electronics and Systems<br/>
        University of A Coruna, 15071 A Coruna, Spain.<br/>
    e-mail: ddarriba@udc.es, dposada@uvigo.es<br/>
<br/>
	<hr/>
	${date} <br/> ${system}<br/>
	
	<p></p> 
	<table align="center">
	<tr valign="top"><td>Citation:</td><td align="left"> Darriba D, Taboada GL, Doallo R and Posada D. 2012. "jModelTest 2: more models, new heuristics and parallel computing". Nature Methods 9, 772.</td></tr>
    </table>
	<p></p>

	 
	Notice: This program may contain errors. Please inspect results carefully.<br/>
	 <br/>
 
</div>

<p class="back-to-top"><a href="#" onclick="scrollTo(0,0);return false;" title="Back to top" class="top"><img src="resources/topIcon.gif" alt="Back to top" class="top" /> Back to top <img src="resources/topIcon.gif" alt="Back to top" class="top" /></a></p>

	<h1><a name="settings"></a>Settings </h1>

		 Arguments = ${arguments}<br/>
		 Input Alignment: "${alignName}"<br/>
		 NumTaxa = ${numTaxa}<br/>
		 Length = ${seqLength}<br/> 
		 Phyml version = ${phymlVersion}<br/>
		 Phyml binary = ${phymlBinary}<br/>
		 Candidate models = ${candidateModels}<br/>
		  number of substitution schemes = ${substSchemes}<br/>
		  <#if includeF == 1>
		  including models with equal/unequal base frequencies (+F)<br/>
		  <#else>
		  including only models with equal base frequencies<br/>
		  </#if>
		  <#if includeI == 1>
		  including models with/without a proportion of invariable sites (+I)<br/>
		  <#else>
		  including only models without a proportion of invariable sites<br/>
		  </#if>
		  <#if includeG == 1>
		  including models with/without rate variation among sites (+G) (nCat = ${numCat})<br/>
		  <#else>
		  including only models without rate variation among sites<br/>
		  </#if>
		 Optimized free parameters (K) = ${freeParameters}<br/>
		 
		 Base tree for likelihood calculations = ${baseTree}<br/>
		 <#if userTreeDef == 1>
		 User tree (${userTreeFilename}) = ${userTree}<br/>
		 </#if>
		 Tree topology search operation = ${searchAlgorithm}<br/>

<p class="back-to-top"><a href="#" onclick="scrollTo(0,0);return false;" title="Back to top" class="top"><img src="resources/topIcon.gif" alt="Back to top" class="top" /> Back to top <img src="resources/topIcon.gif" alt="Back to top" class="top" /></a></p>

<h1> <a name="results"></a>Model Optimization Results </h1>

<div id="sorted-models">
<table class="model-info">
<tr><th> ID </th><th> Name </th><th> Partition </th><th> -lnL </th><th> p </th><th> fA </th><th> fC </th><th> fG </th><th> fT </th><th> ti/tv </th><th> R(a) </th><th> R(b) </th><th> R(c) </th><th> R(d) </th><th> R(e) </th><th> R(f) </th><th> p-inv </th><th> shape </th></tr>
<#list sortedModels as model>
<tr><td> ${model.index}</td><td><a href="http://www.phylowidget.org/full/?tree=${model.tree}&useBranchLengths=true">${model.name}</a></td><td> ${model.partition} </td><td> ${model.lnl} </td><td> ${model.k} </td><td> ${model.fA} </td><td> ${model.fC} </td><td> ${model.fG} </td><td> ${model.fT} </td><td> ${model.titv} </td><td> ${model.rA} </td><td> ${model.rB} </td><td> ${model.rC} </td><td> ${model.rD} </td><td> ${model.rE} </td><td> ${model.rF} </td><td> ${model.pInv} </td><td> ${model.shape} </td></tr>
</#list>
</table>
</div><!--sorted-models-->
<#if isTopologiesSummary == 1>
  <div id="topologies">
  <p>
  There are ${numberOfTopologies} different topologies. The following table shows the models supporting each topology and the rank according to each Information Criterion, as well as Robinson-Foulds and Euclidean distances with the tree of the best-fit model.
  </p>
  <table class="topologies-info">
  <tr><th class="col-id"> ID </th>
      <th class="col-models"> Models </th>
      <th class="col-topo"> Topology </th>
      <th/>
      <th> AIC </th>
      <th> BIC </th>
      <th> AICc </th>
      <th> DT </th>
  </tr>
  <#list sortedTopologies as topology>
  <tr>
    <td rowspan="5" class="col-id"> ${topology.index}</td>
    <td rowspan="5" class="col-models">
    <div class="topo-scroll"> 
      ${topology.models}
    </div>
    </td>
    <td rowspan="5" class="col-topo">
    <div class="topo-scroll">
      <a href="http://www.phylowidget.org/full/?tree=${topology.tree}">${topology.tree}</a>
    </div>
    </td>
    <th>RANK</th>
    <#if isAIC == 1>
      <td class="topo-rank">${topology.aicRank}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isBIC == 1>
      <td class="topo-rank">${topology.bicRank}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isAICc == 1>
      <td class="topo-rank">${topology.aiccRank}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isDT == 1>
      <td class="topo-rank">${topology.dtRank}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    </tr>
    <tr>
    <th>Weight</th>
    <#if isAIC == 1>
      <td class="topo-rank">${topology.aicWeight}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isBIC == 1>
      <td class="topo-rank">${topology.bicWeight}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isAICc == 1>
      <td class="topo-rank">${topology.aiccWeight}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isDT == 1>
      <td class="topo-rank">${topology.dtWeight}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    </tr>
    <tr>
    <th>RF</th>
    <#if isAIC == 1>
      <td class="topo-rank">${topology.aicRF}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isBIC == 1>
      <td class="topo-rank">${topology.bicRF}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isAICc == 1>
      <td class="topo-rank">${topology.aiccRF}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isDT == 1>
      <td class="topo-rank">${topology.dtRF}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    </tr>
    <tr>
    <th>AVG Distance</th>
    <#if isAIC == 1>
      <td class="topo-rank">${topology.aicAvgDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isBIC == 1>
      <td class="topo-rank">${topology.bicAvgDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isAICc == 1>
      <td class="topo-rank">${topology.aiccAvgDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isDT == 1>
      <td class="topo-rank">${topology.dtAvgDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    </tr>
    <tr>
    <th>Distance VAR</th>
    <#if isAIC == 1>
      <td class="topo-rank">${topology.aicVarDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isBIC == 1>
      <td class="topo-rank">${topology.bicVarDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isAICc == 1>
      <td class="topo-rank">${topology.aiccVarDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    <#if isDT == 1>
      <td class="topo-rank">${topology.dtVarDistance}</td>
    <#else>
      <td class="topo-rank"> - </td>
    </#if>
    </tr>
  </#list>
  </table>
  </div><!--sorted-models-->
</#if>
<p class="back-to-top"><a href="#" onclick="scrollTo(0,0);return false;" title="Back to top" class="top"><img src="resources/topIcon.gif" alt="Back to top" class="top" /> Back to top <img src="resources/topIcon.gif" alt="Back to top" class="top" /></a></p>





<#if isAIC == 1>

<div class="selection"> 
<h1> <a name="aic"></a>AIC Selection Results </h1>
<div class="selection-upper"> 
	<div class="selection_best_model">
		<h2 style="text-align: center;"> Model selected </h2>
		<table class="model_info">
		<tr><th>   Model </th><td colspan="2">${bestAicModel.name}</tr>
		<tr><th>   partition </th><td colspan="2"> ${bestAicModel.partition}</tr>
		<tr><th>   -lnL </th><td colspan="2"> ${bestAicModel.lnl}</tr>
		<tr><th>   K </th><td colspan="2"> ${bestAicModel.k}</tr>
		<tr><th>   freqA </th><td> ${bestAicModel.fA}</td><th>   R(a) </th><td> ${bestAicModel.rA} </td></tr>
		<tr><th>   freqC </th><td> ${bestAicModel.fC}</td><th>   R(b) </th><td> ${bestAicModel.rB} </td></tr>
		<tr><th>   freqG </th><td> ${bestAicModel.fG}</td><th>   R(c) </th><td> ${bestAicModel.rC} </td></tr>
		<tr><th>   freqT </th><td> ${bestAicModel.fT}</td><th>   R(d) </th><td> ${bestAicModel.rD} </td></tr>
		<tr><th>   ti/tv </th><td> ${bestAicModel.titv} </td><th>   R(e) </th><td> ${bestAicModel.rE} </td></tr>
		<tr><th></th><td></td><th>   R(f) </th><td> ${bestAicModel.rF} </td></tr>
		<tr><th>   p-inv </th><td> ${bestAicModel.pInv}</td><th>   gamma </th><td> ${bestAicModel.shape} </td></tr>
		</table>
	</div> <!--selection_best_model-->
<div class="selection_best_tree">

	<h2 style="text-align: center;"> Best model tree </h2>
	
		<div class="newick-tree">
		${bestAicModel.tree}
		</div><!--best-tree-newick-->
	<a href="http://www.phylowidget.org/full/?tree=${bestAicModel.tree}&useBranchLengths=true">Display best model tree in PhyloWidget</a>
	</div><!--selection_best_tree-->
</div><!--selection-upper-->

<div class="selection-lower">
<div class="selection_results">
	<table class="selection_table">
		<tr>
		<th>Model</th><th> -lnL  </th><th>  K      </th><th>   AIC </th><th>delta</th><th>   weight</th><th> cumWeight</th>
		</tr>
		<#list aicModels as model>
		<tr><td>
		<a href="http://www.phylowidget.org/full/?tree=${model.tree}&useBranchLengths=true">${model.name}</a> </td><td>${model.lnl}</td><td>${model.k}</td><td>${model.value}</td><td>${model.delta}</td><td>${model.weight}</td><td>${model.cumWeight}</td></tr>
		</#list>
		 </table>
</div><!--selection_results-->
<div class="selection-caption">
<table class="selection_table"><tr><td>
		-lnL:</td><td>negative log likelihod
		 </td> </tr><tr><td>
		 K:</td><td>	number of estimated parameters
		 </td> </tr><tr><td>
		 AIC:</td><td>	Akaike Information Criterion
		 </td> </tr><tr><td>
		 delta:	</td><td>AIC difference
		 </td> </tr><tr><td>
		 weight:</td><td>	AIC weight
		 </td> </tr><tr><td>
		 cumWeight:</td><td>cumulative AIC weight
		 </td> </tr>
	 </table>
<h2>Confidence interval</h2>
 <p class="confidence-list"> 
There are ${aicConfidenceCount} models in the ${confidenceInterval}% confidence interval:<br/>
${aicConfidenceList}
</p>
 </div><!--selection-caption-->
  </div><!--selection-lower-->
  
  <div class="selection-distances">
    <div class="euclidean-img">
    	<img class="distances-img" src="${aicEuImagePath}"/><br/>
    	Euclidean distances histogram from each model optimized tree to <a href="http://www.phylowidget.org/full/?tree=${bestAicModel.tree}&useBranchLengths=true">${bestAicModel.name} tree</a>.
    </div>
    <div class="rf-img">
    	<img class="distances-img" src="${aicRfImagePath}"/><br/>
    	Robinson-Foulds distances histogram from the different topologies to <a href="http://www.phylowidget.org/full/?tree=${bestAicModel.tree}&useBranchLengths=false">${bestAicModel.name} topology</a>.
    </div>
    <div style="clear:both;"></div>
  </div><!--selection-distances-->

<#if isPAUP == 1>
<h2> PAUP block </h2>
${aicPaup}
</#if>
<#if doAICAveragedPhylogeny == 1>
<h2> Model Averaged Phylogeny </h2>

<table style="text-align:left;">
<tr><th>Selection criterion</th><td>AIC</td></tr>
<tr><th>Confidence interval</th><td>${confidenceInterval}%</td></tr>
<tr><th>Consensus type</th><td>${consensusType}</td></tr>
</table>
 
<div class="consensus-tree">
 <div class="newick-tree">
${aicConsensusTree}
		</div><!--newick-tree-->
 <a href="http://www.phylowidget.org/full/?tree=${aicConsensusTree}&useBranchLengths=true">Display consensus tree in PhyloWidget</a>
</div><!--consensus-tree-->
</#if>

<p class="back-to-top"><a href="#" onclick="scrollTo(0,0);return false;" title="Back to top" class="top"><img src="resources/topIcon.gif" alt="Back to top" class="top" /> Back to top <img src="resources/topIcon.gif" alt="Back to top" class="top" /></a></p>

</div><!--selection-->

</#if>

<#if isAICc == 1>

<div class="selection">   
<h1> <a name="aicc"></a>AICc Selection Results </h1>
<div class="selection-upper"> 
	<div class="selection_best_model">
		<h2 style="text-align: center;"> Model selected </h2>
		<table class="model_info">
		<tr><th>   Model </th><td colspan="2">${bestAiccModel.name}</tr>
		<tr><th>   partition </th><td colspan="2"> ${bestAiccModel.partition}</tr>
		<tr><th>   -lnL </th><td colspan="2"> ${bestAiccModel.lnl}</tr>
		<tr><th>   K </th><td colspan="2"> ${bestAiccModel.k}</tr>
		<tr><th>   freqA </th><td> ${bestAiccModel.fA}</td><th>   R(a) </th><td> ${bestAiccModel.rA} </td></tr>
		<tr><th>   freqC </th><td> ${bestAiccModel.fC}</td><th>   R(b) </th><td> ${bestAiccModel.rB} </td></tr>
		<tr><th>   freqG </th><td> ${bestAiccModel.fG}</td><th>   R(c) </th><td> ${bestAiccModel.rC} </td></tr>
		<tr><th>   freqT </th><td> ${bestAiccModel.fT}</td><th>   R(d) </th><td> ${bestAiccModel.rD} </td></tr>
		<tr><th>   ti/tv </th><td> ${bestAiccModel.titv} </td><th>   R(e) </th><td> ${bestAiccModel.rE} </td></tr>
		<tr><th></th><td></td><th>   R(f) </th><td> ${bestAiccModel.rF} </td></tr>
		<tr><th>   p-inv </th><td> ${bestAiccModel.pInv}</td><th>   gamma </th><td> ${bestAiccModel.shape} </td></tr>
		</table>
	</div> <!--selection_best_model-->
<div class="selection_best_tree">

	<h2 style="text-align: center;"> Best model tree </h2>
	
		<div class="newick-tree">
		${bestAiccModel.tree}
		</div><!--best-tree-newick-->
	<a href="http://www.phylowidget.org/full/?tree=${bestAiccModel.tree}&useBranchLengths=true">Display best model tree in PhyloWidget</a>
	</div><!--selection_best_tree-->
</div><!--selection-upper-->

<div class="selection-lower">
<div class="selection_results">
	<table class="selection_table">
		<tr>
		<th>Model</th><th> -lnL  </th><th>  K      </th><th>   AICc </th><th>delta</th><th>   weight</th><th> cumWeight</th>
		</tr>
		<#list aiccModels as model>
		<tr><td>
		<a href="http://www.phylowidget.org/full/?tree=${model.tree}&useBranchLengths=true">${model.name}</a> </td><td>${model.lnl}</td><td>${model.k}</td><td>${model.value}</td><td>${model.delta}</td><td>${model.weight}</td><td>${model.cumWeight}</td></tr>
		</#list>
		 </table>
</div><!--selection_results-->
<div class="selection-caption">
<table class="selection_table"><tr><td>
		-lnL:</td><td>negative log likelihod
		 </td> </tr><tr><td>
		 K:</td><td>	number of estimated parameters
		 </td> </tr><tr><td>
		 AICc:</td><td>	Corrected Akaike Information Criterion
		 </td> </tr><tr><td>
		 delta:	</td><td>AICc difference
		 </td> </tr><tr><td>
		 weight:</td><td>	AICc weight
		 </td> </tr><tr><td>
		 cumWeight:</td><td>cumulative AICc weight
		 </td> </tr>
	 </table>
<h2>Confidence interval</h2>
 <p class="confidence-list"> 
There are ${aiccConfidenceCount} models in the ${confidenceInterval}% confidence interval:<br/>
${aiccConfidenceList}
</p>
 </div><!--selection-caption-->
  </div><!--selection-lower-->
  
  <div class="selection-distances">
    <div class="euclidean-img">
    	<img class="distances-img" src="${aiccEuImagePath}"/><br/>
    	Euclidean distances histogram from each model optimized tree to <a href="http://www.phylowidget.org/full/?tree=${bestAiccModel.tree}&useBranchLengths=true">${bestAiccModel.name} tree</a>.
    </div>
    <div class="rf-img">
    	<img class="distances-img" src="${aiccRfImagePath}"/><br/>
    	Robinson-Foulds distances histogram from the different topologies to <a href="http://www.phylowidget.org/full/?tree=${bestAiccModel.tree}&useBranchLengths=false">${bestAiccModel.name} topology</a>.
    </div>
    <div style="clear:both;"></div>
  </div><!--selection-distances-->
<#if isPAUP == 1>
<h2> PAUP block </h2>
${aiccPaup}
</#if>
<#if doAICcAveragedPhylogeny == 1>
<h2> Model Averaged Phylogeny </h2>

<table style="text-align:left;">
<tr><th>Selection criterion</th><td>AICc</td></tr>
<tr><th>Confidence interval</th><td>${confidenceInterval}%</td></tr>
<tr><th>Consensus type</th><td>${consensusType}</td></tr>
</table>
 
<div class="consensus-tree">
 <div class="newick-tree">
${aiccConsensusTree}
		</div><!--newick-tree-->
 <a href="http://www.phylowidget.org/full/?tree=${aiccConsensusTree}&useBranchLengths=true">Display consensus tree in PhyloWidget</a>
</div><!--consensus-tree-->
</#if>

</div><!--selection-->

<p class="back-to-top"><a href="#" onclick="scrollTo(0,0);return false;" title="Back to top" class="top"><img src="resources/topIcon.gif" alt="Back to top" class="top" /> Back to top <img src="resources/topIcon.gif" alt="Back to top" class="top" /></a></p>

</#if>




<#if isBIC == 1>

<div class="selection">   
<h1> <a name="bic"></a>BIC Selection Results </h1>
<div class="selection-upper"> 
	<div class="selection_best_model">
		<h2 style="text-align: center;"> Model selected </h2>
		<table class="model_info">
		<tr><th>   Model </th><td colspan="2">${bestBicModel.name}</tr>
		<tr><th>   partition </th><td colspan="2"> ${bestBicModel.partition}</tr>
		<tr><th>   -lnL </th><td colspan="2"> ${bestBicModel.lnl}</tr>
		<tr><th>   K </th><td colspan="2"> ${bestBicModel.k}</tr>
		<tr><th>   freqA </th><td> ${bestBicModel.fA}</td><th>   R(a) </th><td> ${bestBicModel.rA} </td></tr>
		<tr><th>   freqC </th><td> ${bestBicModel.fC}</td><th>   R(b) </th><td> ${bestBicModel.rB} </td></tr>
		<tr><th>   freqG </th><td> ${bestBicModel.fG}</td><th>   R(c) </th><td> ${bestBicModel.rC} </td></tr>
		<tr><th>   freqT </th><td> ${bestBicModel.fT}</td><th>   R(d) </th><td> ${bestBicModel.rD} </td></tr>
		<tr><th>   ti/tv </th><td> ${bestBicModel.titv} </td><th>   R(e) </th><td> ${bestBicModel.rE} </td></tr>
		<tr><th></th><td></td><th>   R(f) </th><td> ${bestBicModel.rF} </td></tr>
		<tr><th>   p-inv </th><td> ${bestBicModel.pInv}</td><th>   gamma </th><td> ${bestBicModel.shape} </td></tr>
		</table>
	</div> <!--selection_best_model-->
<div class="selection_best_tree">

	<h2 style="text-align: center;"> Best model tree </h2>
	
		<div class="newick-tree">
		${bestBicModel.tree}
		</div><!--best-tree-newick-->
	<a href="http://www.phylowidget.org/full/?tree=${bestBicModel.tree}&useBranchLengths=true">Display best model tree in PhyloWidget</a>
	</div><!--selection_best_tree-->
</div><!--selection-upper-->

<div class="selection-lower">
<div class="selection_results">
	<table class="selection_table">
		<tr>
		<th>Model</th><th> -lnL  </th><th>  K      </th><th>   BIC </th><th>delta</th><th>   weight</th><th> cumWeight</th>
		</tr>
		<#list bicModels as model>
		<tr><td>
		<a href="http://www.phylowidget.org/full/?tree=${model.tree}&useBranchLengths=true">${model.name}</a> </td><td>${model.lnl}</td><td>${model.k}</td><td>${model.value}</td><td>${model.delta}</td><td>${model.weight}</td><td>${model.cumWeight}</td></tr>
		</#list>
		 </table>
</div><!--selection_results-->
<div class="selection-caption">
<table class="selection_table"><tr><td>
		-lnL:</td><td>negative log likelihod
		 </td> </tr><tr><td>
		 K:</td><td>	number of estimated parameters
		 </td> </tr><tr><td>
		 BIC:</td><td>	Bayesian Information Criterion
		 </td> </tr><tr><td>
		 delta:	</td><td>BIC difference
		 </td> </tr><tr><td>
		 weight:</td><td>	BIC weight
		 </td> </tr><tr><td>
		 cumWeight:</td><td>cumulative BIC weight
		 </td> </tr>
	 </table>
<h2>Confidence interval</h2>
 <p class="confidence-list"> 
There are ${bicConfidenceCount} models in the ${confidenceInterval}% confidence interval:<br/>
${bicConfidenceList}
</p>
  </div><!--selection-caption-->
  </div><!--selection-lower-->

  <div class="selection-distances">
    <div class="euclidean-img">
    	<img class="distances-img" src="${bicEuImagePath}"/><br/>
    	Euclidean distances histogram from each model optimized tree to <a href="http://www.phylowidget.org/full/?tree=${bestBicModel.tree}&useBranchLengths=true">${bestBicModel.name} tree</a>.
    </div>
    <div class="rf-img">
    	<img class="distances-img" src="${bicRfImagePath}"/><br/>
    	Robinson-Foulds distances histogram from the different topologies to <a href="http://www.phylowidget.org/full/?tree=${bestBicModel.tree}&useBranchLengths=false">${bestBicModel.name} topology</a>.
    </div>
    <div style="clear:both;"></div>
  </div><!--selection-distances-->
<#if isPAUP == 1>
<h2> PAUP block </h2>
${bicPaup}
</#if>
<#if doBICAveragedPhylogeny == 1>
<h2> Model Averaged Phylogeny </h2>

<table style="text-align:left;">
<tr><th>Selection criterion</th><td>BIC</td></tr>
<tr><th>Confidence interval</th><td>${confidenceInterval}%</td></tr>
<tr><th>Consensus type</th><td>${consensusType}</td></tr>
</table>
 
<div class="consensus-tree">
 <div class="newick-tree">
${bicConsensusTree}
		</div><!--newick-tree-->
 <a href="http://www.phylowidget.org/full/?tree=${bicConsensusTree}&useBranchLengths=true">Display consensus tree in PhyloWidget</a>
</div><!--consensus-tree-->
</#if>

<p class="back-to-top"><a href="#" onclick="scrollTo(0,0);return false;" title="Back to top" class="top"><img src="resources/topIcon.gif" alt="Back to top" class="top" /> Back to top <img src="resources/topIcon.gif" alt="Back to top" class="top" /></a></p>

</div><!--selection-->

</#if>



<#if isDT == 1>

<div class="selection">   
<h1> <a name="dt"></a>Decision Theory Selection Results </h1>
<div class="selection-upper">
	<div class="selection_best_model">
		<h2 style="text-align: center;"> Model selected </h2>
		<table class="model_info">
		<tr><th>   Model </th><td colspan="2">${bestDtModel.name}</tr>
		<tr><th>   partition </th><td colspan="2"> ${bestDtModel.partition}</tr>
		<tr><th>   -lnL </th><td colspan="2"> ${bestDtModel.lnl}</tr>
		<tr><th>   K </th><td colspan="2"> ${bestDtModel.k}</tr>
		<tr><th>   freqA </th><td> ${bestDtModel.fA}</td><th>   R(a) </th><td> ${bestDtModel.rA} </td></tr>
		<tr><th>   freqC </th><td> ${bestDtModel.fC}</td><th>   R(b) </th><td> ${bestDtModel.rB} </td></tr>
		<tr><th>   freqG </th><td> ${bestDtModel.fG}</td><th>   R(c) </th><td> ${bestDtModel.rC} </td></tr>
		<tr><th>   freqT </th><td> ${bestDtModel.fT}</td><th>   R(d) </th><td> ${bestDtModel.rD} </td></tr>
		<tr><th>   ti/tv </th><td> ${bestDtModel.titv} </td><th>   R(e) </th><td> ${bestDtModel.rE} </td></tr>
		<tr><th></th><td></td><th>   R(f) </th><td> ${bestDtModel.rF} </td></tr>
		<tr><th>   p-inv </th><td> ${bestDtModel.pInv}</td><th>   gamma </th><td> ${bestDtModel.shape} </td></tr>
		</table>
	</div> <!--selection_best_model-->
<div class="selection_best_tree">

	<h2 style="text-align: center;"> Best model tree </h2>
	
		<div class="newick-tree">
		${bestDtModel.tree}
		</div><!--best-tree-newick-->
	<a href="http://www.phylowidget.org/full/?tree=${bestDtModel.tree}&useBranchLengths=true">Display best model tree in PhyloWidget</a>
	</div><!--selection_best_tree-->
</div><!--selection-upper-->

<div class="selection-lower">
<div class="selection_results">
	<table class="selection_table">
		<tr>
		<th>Model</th><th> -lnL  </th><th>  K      </th><th>   DT </th><th>delta</th><th>   weight</th><th> cumWeight</th>
		</tr>
		<#list dtModels as model>
		<tr><td>
		<a href="http://www.phylowidget.org/full/?tree=${model.tree}&useBranchLengths=true">${model.name}</a> </td><td>${model.lnl}</td><td>${model.k}</td><td>${model.value}</td><td>${model.delta}</td><td>${model.weight}</td><td>${model.cumWeight}</td></tr>
		</#list>
		 </table>
</div><!--selection_results-->
<div class="selection-caption">
<table class="selection_table"><tr><td>
		-lnL:</td><td>negative log likelihod
		 </td> </tr><tr><td>
		 K:</td><td>	number of estimated parameters
		 </td> </tr><tr><td>
		 DT:</td><td>	Akaike Information Criterion
		 </td> </tr><tr><td>
		 delta:	</td><td>DT difference
		 </td> </tr><tr><td>
		 weight:</td><td>	DT weight
		 </td> </tr><tr><td>
		 cumWeight:</td><td>cumulative DT weight
		 </td> </tr>
	 </table>
<h2>Confidence interval</h2>
 <p class="confidence-list"> 
There are ${dtConfidenceCount} models in the ${confidenceInterval}% confidence interval:<br/>
${dtConfidenceList}
</p>
 </div><!--selection-caption-->
  </div><!--selection-lower-->
  
  <div class="selection-distances">
    <div class="euclidean-img">
    	<img class="distances-img" src="${dtEuImagePath}"/><br/>
    	Euclidean distances histogram from each model optimized tree to <a href="http://www.phylowidget.org/full/?tree=${bestDtModel.tree}&useBranchLengths=true">${bestDtModel.name} tree</a>.
    </div>
    <div class="rf-img">
    	<img class="distances-img" src="${dtRfImagePath}"/><br/>
    	Robinson-Foulds distances histogram from the different topologies to <a href="http://www.phylowidget.org/full/?tree=${bestDtModel.tree}&useBranchLengths=false">${bestDtModel.name} topology</a>.
    </div>
    <div style="clear:both;"></div>
  </div><!--selection-distances-->
  <#if isPAUP == 1>
    <h2> PAUP block </h2>
    ${dtPaup}
  </#if>
<#if doDTAveragedPhylogeny == 1>
<h2> Model Averaged Phylogeny </h2>

<table style="text-align:left;">
<tr><th>Selection criterion</th><td>DT</td></tr>
<tr><th>Confidence interval</th><td>${confidenceInterval}%</td></tr>
<tr><th>Consensus type</th><td>${consensusType}</td></tr>
</table>
 
<div class="consensus-tree">
 <div class="newick-tree">
${dtConsensusTree}
		</div><!--newick-tree-->
 <a href="http://www.phylowidget.org/full/?tree=${dtConsensusTree}&useBranchLengths=true">Display consensus tree in PhyloWidget</a>
</div><!--consensus-tree-->
</#if>

<p class="back-to-top"><a href="#" onclick="scrollTo(0,0);return false;" title="Back to top" class="top"><img src="resources/topIcon.gif" alt="Back to top" class="top" /> Back to top <img src="resources/topIcon.gif" alt="Back to top" class="top" /></a></p>

</div><!--selection-->

</#if>





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